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- PDB-7t5i: Crystal Structure of Strictosidine Synthase in complex with R-IPA... -

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Basic information

Entry
Database: PDB / ID: 7t5i
TitleCrystal Structure of Strictosidine Synthase in complex with R-IPA(2-(1H-indol-3-yl) propan-1-amine)
ComponentsStrictosidine synthase
KeywordsLYASE / ALKALOID METABOLISM / SIX BLADED BETA PROPELLER FOLD / STR1 / VACUOLE / SYNTHASE / GLYCOPROTEIN
Function / homology
Function and homology information


strictosidine synthase / strictosidine synthase activity / alkaloid metabolic process / vacuole / biosynthetic process / endomembrane system / hydrolase activity
Similarity search - Function
Strictosidine synthase, conserved region / Strictosidine synthase / Six-bladed beta-propeller, TolB-like
Similarity search - Domain/homology
(2R)-2-(1H-indol-3-yl)propan-1-amine / Strictosidine synthase
Similarity search - Component
Biological speciesRauvolfia serpentina (serpentwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsLiu, H. / Panjikar, S. / Futamura, Y. / Shao, N. / Osada, H. / Zou, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21472170 China
Citation
Journal: to be published
Title: Beta-Branched Tryptamine Provoked Non Sandwich-Like-Mode Catalysis of Strictosidine Synthase to Antimalarial Indole Alkaloids
Authors: Liu, H. / Panjikar, S. / Futamura, Y. / Shao, N. / Osada, H. / Zou, H.
#1: Journal: Plant Cell / Year: 2006
Title: The structure of Rauvolfia serpentina strictosidine synthase is a novel six-bladed beta-propeller fold in plant proteins.
Authors: Ma, X. / Panjikar, S. / Koepke, J. / Loris, E. / Stoeckigt, J.
History
DepositionDec 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Strictosidine synthase
B: Strictosidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7634
Polymers70,4152
Non-polymers3482
Water724
1
A: Strictosidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3822
Polymers35,2071
Non-polymers1741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Strictosidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3822
Polymers35,2071
Non-polymers1741
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.305, 150.305, 121.562
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 2 / Auth seq-ID: 33 - 324 / Label seq-ID: 5 - 296

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.957749, -0.161825, -0.23776), (-0.014926, -0.797606, 0.602994), (-0.287218, 0.581065, 0.761491)84.56055, 120.70254, -31.57642

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Components

#1: Protein Strictosidine synthase


Mass: 35207.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rauvolfia serpentina (serpentwood) / Gene: STR1 / Plasmid: PQE-2 / Production host: Escherichia coli (E. coli) / Strain (production host): M15PREP4 / References: UniProt: P68175, strictosidine synthase
#2: Chemical ChemComp-XL4 / (2R)-2-(1H-indol-3-yl)propan-1-amine


Mass: 174.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H14N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.72 Å3/Da / Density % sol: 66.93 % / Description: Hexagonal
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.8 M POTASSIUM SODIUM TARTRATE TETRAHYDRATE AND 0.1 M HEPES, PH 7.4, 5 MG/ML STRICTOSIDINE and 3 mM R-IPA (2-(1H-indol-3-yl) propan-1-amine),

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 25, 2017 / Details: DCM
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.94→20 Å / Num. obs: 21817 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 74.76 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.029 / Rrim(I) all: 0.098 / Net I/σ(I): 20
Reflection shellResolution: 2.94→3.02 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.602 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 1626 / CC1/2: 0.639 / Rrim(I) all: 0.632 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
Aimlessdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FP8

2fp8


Resolution: 2.94→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.929 / SU B: 30.054 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R: 0.915 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2189 956 4.4 %RANDOM
Rwork0.16726 ---
obs0.16955 20762 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.202 Å2
Baniso -1Baniso -2Baniso -3
1-3.33 Å21.67 Å20 Å2
2--3.33 Å20 Å2
3----10.82 Å2
Refinement stepCycle: 1 / Resolution: 2.94→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4800 0 26 4 4830
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124960
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.6326750
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5565608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8823.71248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.51915774
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8761516
X-RAY DIFFRACTIONr_chiral_restr0.1140.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023868
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3325.282438
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.1769.9043044
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.2925.5432522
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.78473.7877260
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1139medium positional0.240.5
1168tight thermal4.220.5
1139medium thermal5.072
LS refinement shellResolution: 2.94→3.014 Å
RfactorNum. reflection% reflection
Rfree0.255 65 -
Rwork0.248 1531 -
obs--99.75 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6942-0.59760.29344.48370.66914.14750.05040.2199-0.0964-0.03960.0504-0.18570.18950.5895-0.10080.01570.0483-0.0060.1705-0.03730.020939.353545.7772-8.5812
25.05631.7833-1.67161.8207-0.48535.0999-0.10650.3731-0.37910.27170.15130.05960.6951-0.1454-0.04490.2620.0387-0.03960.0498-0.05880.123730.671833.47620.659
32.46420.3051-0.69823.7622-0.81643.15240.1423-0.0007-0.11240.3081-0.05550.04810.23740.2539-0.08680.11230.0555-0.0060.0448-0.00390.011931.930346.58711.0931
41.85541.655-1.34873.11470.88396.7226-0.1646-0.08980.21930.1218-0.07940.417-0.4209-0.43560.2440.31270.1354-0.00270.1486-0.01530.175833.171658.32560.8756
53.1132-0.7842-2.21613.2359-0.44247.88490.1250.2657-0.2714-0.1635-0.2040.0097-0.1717-0.18650.0790.0811-0.0688-0.00690.1487-0.04540.107436.995273.7508-13.861
61.0999-0.5306-0.92654.06151.88224.29970.30040.14140.4368-0.5353-0.2514-0.3701-0.7942-0.0989-0.0490.33410.00030.05650.16830.01330.327139.569793.5848-12.6482
71.4156-2.9393-1.26336.12762.38924.10360.0506-0.10150.2113-0.140.2433-0.4343-0.12460.0631-0.29390.3123-0.0395-0.05590.4301-0.05530.442757.127287.01753.3003
80.8251-0.3794-0.96277.25411.87633.78040.0044-0.25610.12220.20080.1307-0.2908-0.1080.3478-0.1350.1148-0.0822-0.0710.2028-0.06040.148138.801583.37812.5159
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 157
2X-RAY DIFFRACTION2A158 - 209
3X-RAY DIFFRACTION3A210 - 319
4X-RAY DIFFRACTION4A320 - 333
5X-RAY DIFFRACTION5B32 - 92
6X-RAY DIFFRACTION6B93 - 270
7X-RAY DIFFRACTION7B271 - 280
8X-RAY DIFFRACTION8B281 - 333

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